Citrate Synthase

The Structure and Mechanism of Citrate Synthase
 Citrate synthase is an enzyme active in all examined cells, where it is most often responsible for catalyzing the first reaction of the citric acid cycle (Krebs Cycle or the tricarboxylic acid [ TCA ] cycle): the condensation of acetyl-CoA and oxaloacetate to form citrate. Although in eukaryotes it is a mitochondrial enzyme, and in fact, is often used as a enzyme marker for intact mitochondria, it is encoded by nuclear DNA. The standard free energy change (ΔG°’) for the citrate synthase reaction is -31.5kJ/mol. This negative free energy value means that citrate synthase is likely to function far from equilibrium under physiological conditions, and is thus a rate-determining enzyme in the citric acid cycle. Structure: Biologically, citrate synthase exists as a homodimer of a single amino acid chain monomer. Each identical subunit consists of a large and a small domain, and is comprised almost entirely of α helices (making it an all α protein). In its free enzyme state, citrate synthase exists in an “open” form of the homodimer, with its two domains forming a cleft containing the substrate (oxaloacetate) binding site (PDB: 1cts). When oxaloacetate binds, the smaller domain undergoes an 18° rotation, sealing the oxaloacetate binding site and resulting in the closed conformation of the homodimer (PDB: 2cts). The dramatic conformational change is best illustrated via a morph between the "open" and "closed" states, and be sure to view the morph from the side as well to get a full sense of the structural change. The conformational change not only prevents solvent from reaching the bound substrate, but also generates the acetyl-CoA binding site. This presence of “open” and “closed” forms results in citrate synthase having Ordered Sequential kinetic behavior.

 

3D structures of Citrate Synthase
Update June 2011

3msu – CitS – Francisella tularensis

3enj – CitS – Wild boar

2p2w – CitS – Thermotoga maritima

2c6x – CitS residues 2-364 – Bacillus subtilis

3l96, 1owc, 1nxe – EcCitS (mutant) – Eschericia coli

1k3p – EcCitS II

2ibp – CitS – Pyrobaculum aerophilum

1iom, 1ixe – CitS – Thermus thermophilus

1o7x – CitS – Sulfolobus solfataricus

1a59 – CitS – Antarctic bacterium

1aj8 – CitS - Pyrococcus furiosus

5csc, 3cts – cCitS – chicken

1cts, 2cts – pCitS - pig

Citrate synthase binary complex
3l97 - EcCitS (mutant) + S-carboxymethyl-CoA

2r9e – TaCitS + citryl dethia CoA – Thermoplasma acidophilum

6cts – cCitS + citryl thioether CoA

3l98, 1owb, 1nxg - EcCitS (mutant) + NADH

3l99 - EcCitS (mutant) + oxaloacetate

2ifc - TaCitS + oxaloacetate

Citrate synthase ternary complex
2r26 - TaCitS + oxaloacetate + S-carboxymethyl-CoA

2h12 - CitS + oxaloacetate + carboxymethyl dethia-CoA – Acetobacter aceti

1al6, 1csr, 1css, 1csh, 1csi - cCitS + oxaloacetate + carboxymethyl dethia-CoA derivative

5cts - cCitS + oxaloacetate + carboxymethyl CoA

1amz - cCitS + malate + nitromethyl dethia-CoA

1csc, 2csc, 3csc, 4csc - cCitS + malate + carboxymethyl CoA

6csc - cCitS + citrate + trifluoroacetonyl-CoA

4cts - pCitS + oxaloacetate + S-acetonyl CoA

External Resources

 * Citrate Synthase: September 2007 Molecule of the Month as part of the series of tutorials that are at the RCSB Protein Data Bank and written by David Goodsell
 * |00510|00520|00530|00540|00550|00PRS|00010|00020|00030|00040|00050|00060|00070|00080|00090|00100|00110|00120|01000|02000|03000|04000|05000|06000|07000|08000|09000|10000|11000|12000|13000|14000|15000|16000|17000|18000|19000|20000|21000|22000|23000|24000|25000|26000|27000|28000|99000|&ns=0&t=&uid=0&rau=0 An interactive schematic animation of Citrate synthase's reaction mechanism from Lehninger's Principles of Biochemistry
 * Citrate Synthase at Wikipedia